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Welcome to the GenomeWeb Nucleic Acid Multiple Sequence Analysis Search for:

THE MEME SYSTEM - Multiple EM for Motif Elicitation
Meta-MEME motif-based hidden Markov models

Detailed information on the above options

THE MEME SYSTEM - Multiple EM for Motif Elicitation
MEME is a tool for discovering motifs in a group of related DNA or protein sequences.

A motif is a sequence pattern that occurs repeatedly in a group of related protein or DNA sequences. MEME represents motifs as position-dependent letter-probability matrices which describe the probability of each possible letter at each position in the pattern. Individual MEME motifs do not contain gaps. Patterns with variable-length gaps are split by MEME into two or more separate motifs.

MEME takes as input a group of DNA or protein sequences (the training set) and outputs as many motifs as requested. MEME uses statistical modeling techniques to automatically choose the best width and description for each motif.

Meta-MEME motif-based hidden Markov models
Meta-MEME is a software toolkit for building and using motif-based hidden Markov models of DNA and proteins. The input to Meta-MEME is a set of similar protein sequences, as well as a set of motif models discovered by MEME. Meta-MEME combines these models into a single, motif-based hidden Markov model and uses this model to produce a multiple alignment of the original set of sequences and to search a sequence database for homologs.